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- PDB-4oeh: X-ray Structure of Uridine Phosphorylase from Vibrio cholerae Com... -

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Basic information

Entry
Database: PDB / ID: 4oeh
TitleX-ray Structure of Uridine Phosphorylase from Vibrio cholerae Complexed with Uracil at 1.91 A Resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Rossmann fold / Nucleoside
Function / homology
Function and homology information


nucleotide catabolic process / uridine phosphorylase / uridine phosphorylase activity / UMP salvage / nucleoside catabolic process / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Uridine phosphorylase / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ETHANOL / DI(HYDROXYETHYL)ETHER / URACIL / Uridine phosphorylase / Uridine phosphorylase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.91 Å
AuthorsProkofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
CitationJournal: To Be Published / Year: 2016
Title: X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases.
Authors: Prokofev, I.I. / Lashkov, A.A. / Balaev, T. / Seregina, A.S. / Mironov, C. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
History
DepositionJan 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Other
Revision 1.2Jan 11, 2017Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Database references / Refinement description
Category: citation_author / diffrn_source / refine
Item: _citation_author.name / _diffrn_source.pdbx_synchrotron_site ..._citation_author.name / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type / _refine.ls_R_factor_all / _refine.pdbx_starting_model
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uridine phosphorylase
B: Uridine phosphorylase
C: Uridine phosphorylase
D: Uridine phosphorylase
E: Uridine phosphorylase
F: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,30928
Polymers162,6546
Non-polymers1,65522
Water22,9691275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25540 Å2
ΔGint-85 kcal/mol
Surface area46100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.255, 71.763, 89.321
Angle α, β, γ (deg.)69.140, 72.150, 85.790
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Uridine phosphorylase


Mass: 27108.994 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: 569B / Gene: udp, VC_1034 / Plasmid: pMZ21 / Production host: Escherichia coli (E. coli) / Strain (production host): Am201
References: UniProt: Q9KT71, UniProt: Q9K4U1*PLUS, uridine phosphorylase

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Non-polymers , 7 types, 1297 molecules

#2: Chemical
ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H4N2O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1275 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Magnesium chloride hexahydrate, TRIS hydrochloride, PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.907→79.6 Å / Num. all: 104334 / Num. obs: 99133 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Rsym value: 0.065 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.91-2.011.80.4091.927074150430.40992.8
2.01-2.131.80.2882.725029142860.28893.9
2.13-2.281.80.1944.124037135210.19494.3
2.28-2.461.80.1365.822831126500.13694.6
2.46-2.71.70.097820343116710.09794.8
2.7-3.021.80.06212.619221105860.06295.4
3.02-3.481.80.03919.61649693590.03995.6
3.48-4.271.80.027251424079200.02795.6
4.27-6.031.70.028241040159480.02893.2
6.03-44.2781.80.0233.4602833500.0295.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
MOLREPphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
DNAdata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H1T

1h1t


Resolution: 1.91→44.278 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.1979 / WRfactor Rwork: 0.156 / FOM work R set: 0.8636 / SU B: 7.165 / SU ML: 0.109 / SU R Cruickshank DPI: 0.1768 / SU Rfree: 0.1541 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 5198 5 %RANDOM
Rwork0.1722 ---
obs0.1744 99133 94.37 %-
all-104331 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.43 Å2 / Biso mean: 23.226 Å2 / Biso min: 9 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.81 Å20.52 Å2
2---0.19 Å20.99 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 1.91→44.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11258 0 109 1275 12642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01911776
X-RAY DIFFRACTIONr_angle_refined_deg1.1541.96315981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.38451570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.35323.734466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41151978
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1381582
X-RAY DIFFRACTIONr_chiral_restr0.0780.21882
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218790
LS refinement shellResolution: 1.907→1.957 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 397 -
Rwork0.293 7111 -
all-7508 -
obs--91.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5264-0.04580.00080.1226-0.04410.4413-0.00670.03710.0586-0.01720.00730.0055-0.0687-0.0526-0.00070.04980.0131-0.01520.02680.0220.0355-10.40918.98-18.013
20.1850.0389-0.03040.4970.03220.44390.00370.0070.03480.0057-0.01840.0495-0.0621-0.1050.01470.02920.0244-0.00910.03480.00420.0463-19.53519.25.465
30.36270.0634-0.37840.58670.00230.5743-0.0017-0.0848-0.00320.0997-0.0220.00950.0220.07230.02360.0482-0.0023-0.00780.04050.00930.0111-4.4413.38727.605
40.4453-0.01840.40510.41810.09740.65240.0358-0.0712-0.04680.109-0.016-0.00710.1193-0.0028-0.01980.08150.0015-0.01250.04510.02760.02158.884-17.64920.19
50.19830.00440.12290.56330.0520.35550.00480.0055-0.02650.00450.0116-0.0480.0440.051-0.01630.01610.01130.00030.02040.00330.036819.163-18.089-9.187
60.6801-0.0651-0.36850.1036-0.05540.5096-0.01110.0855-0.0658-0.0346-0.02280.01310.0274-0.02830.03390.0321-0.0034-0.0080.0278-0.00370.01725.826-5.934-26.978
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 253
2X-RAY DIFFRACTION2B2 - 253
3X-RAY DIFFRACTION3C3 - 253
4X-RAY DIFFRACTION4D3 - 253
5X-RAY DIFFRACTION5E3 - 253
6X-RAY DIFFRACTION6F3 - 253

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